Methods for isolating a peptide methods for identifying a peptide

Abstract

The present invention is directed to methods, for example phage display assays, for bioengineering peptides that bind to individual distinct nucleotides. Also provided are peptides engineered by such methods. Specifically, cyclic peptides that bind individual distinct nucleotides are provided herein.

The invention claimed is: 
     
       1. A method for identifying a peptide comprising:
 incubating a first peptide library with a first set of nucleic acid oligonucleotides to identify a first sub-library of peptides that bind the first set of nucleic acid oligonucleotides; 
 separating the first sub-library from the first library; 
 contacting the first sub-library with a second set of nucleic acid oligonucleotides comprising homo-oligomers of nucleotides other than a preselected nucleotide, to identify a second sub-library of peptides that do not bind the second set of nucleic acid oligonucleotides; 
 separating the second sub-library from the first sub-library; 
 contacting the second sub-library with a third subset of nucleic acid oligonucleotides comprising a homogeneous population of homo-oligonucleotides comprising the pre-selected nucleotide and no other nucleotides, to identify a third sub-library of peptides that bind to the third subset of nucleic acid oligonucleotides; 
 separating the third sub-library from the second sub-library; 
 contacting the third sub-library with a plurality of a first set of aminolated nucleotides comprising a heterogeneous population of nucleotides other than the pre-selected nucleotide, to identify a fourth sub-library of peptides that do not bind the first set of aminolated nucleotides; 
 separating the fourth sub-library from the fifth sub-library; and 
 contacting the fifth sub-library with a second set of aminolated nucleotides, comprising a homogeneous population of the pre-selected nucleotide, to produce a sixth sub-library of peptides that bind the second set of aminolated nucleotides, thereby identifying a peptide that binds the pre-selected nucleotide. 
 
     
     
       2. “The method of  claim 1 , wherein at least one of the separations is carried out with a solid phase.” 
     
     
       3. “The method of  claim 2 , wherein the solid phase comprises magnetic particles.” 
     
     
       4. “The method of  claim 1 , wherein the first peptide library comprises a cyclic peptide phage display library.” 
     
     
       5. “The method of  claim 1 , wherein the pre-selected nucleotide comprises a non-natural or a natural nucleotide.” 
     
     
       6. “The method of  claim 1 , wherein the homo-oligonucleotides comprise five to ten nucleotides.”